---
layout: post
title: N50 with conda
---

This tiny post is to celebrate my first [Bioconda](https://bioconda.github.io/) release,
the handy **n50** utility, that as the name implies calculates N50 from either FASTA or
FASTQ files. The main use I did of this script was to quickly feed the output in bash scripts
like:

    CHECK=$(n50 contigs.fasta)

But now it has a whole range of output options including JSON, TSV, CSV and this fancy 
human friendly alternative:

    .----------------------------------------------------------------.
    | File               | Seqs   | Total bp   | N50   | min | max   |
    +--------------------+--------+------------+-------+-----+-------+
    | test_fasta_grep.fa |      1 |         80 |    80 |  80 |    80 |
    | small_test.fa      |      6 |        130 |    65 |   4 |    65 |
    | rdp_16s_v16.fa     | 13,212 | 19,098,167 | 1,467 | 320 | 2,210 |
    '--------------------+--------+------------+-------+-----+-------'

## How to get it

From Miniconda:
![Install with Conda](https://anaconda.org/bioconda/n50/badges/installer/conda.svg) 
![Conda (channel only)](https://img.shields.io/conda/vn/bioconda/n50?style=social)

    conda install -c bioconda n50

or with CPANminus:

    cpanm Proch::N50